Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems

Abstract

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, ‘Candidatus Thiothrix moscowensis’ and ‘Candidatus Thiothrix singaporensis’. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO2 assimilation through the Calvin–Benson–Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms.

Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

“…The genus Thiothrix is relatively poorly studied due to the small number of described species, the complexity of cultivation, as well as the limited number of genomic sequences and high-quality MAGs. In this work and previously (Mardanov et al, 2020) we…”

“…Metagenomic analysis of groundwater and cave lakes has shown the presence of representatives of the genus Thiothrix (Macalady et al, 2008;Rossmassler et al, 2016;Panova et al, 2020). Also members of this genus were found in hydrothermal marine ecosystems, wastewater treatment bioreactors (Mardanov et al, 2020), and as ectosymbionts of invertebrates (Konkol et al, 2010;Bauermeister et al, 2012;Li et al, 2018). However, no pure cultures were obtained from these biotopes.…”

“…After the last taxonomic revision (Boden and Scott, 2018) the genus Thiothrix includes five species: Thiothrix nivea (Larkin and Shinabarger, 1983), T. fructosivorans, Thiothrix unzii (Howarth et al, 1999), T. caldifontis, and T. lacustris (Chernousova et al, 2010). In addition, two Thiothrix MAGs were obtained from laboratory-scale enhanced biological phosphorus removal bioreactors (Mardanov et al, 2020). These MAGs represent two new species referred to as "Candidatus Thiothrix moscowensis" RT and "Candidatus Thiothrix singaporensis" SSD2 (Mardanov et al, 2020).…”

“…In addition, two Thiothrix MAGs were obtained from laboratory-scale enhanced biological phosphorus removal bioreactors (Mardanov et al, 2020). These MAGs represent two new species referred to as "Candidatus Thiothrix moscowensis" RT and "Candidatus Thiothrix singaporensis" SSD2 (Mardanov et al, 2020). Therefore, obtaining new isolates and MAGs, especially from atypical habitats, could expand our knowledge of the diversity of Thiothrix and would allow to identify new species of this genus.…”

The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow

“…Dechloromonas sp., denitrifying bacteria capable of acetate uptake and polyphosphate storage, accounted for 1.5% to 5.8% of AS microbiomes in bioreactors operating under aerobic and UCT processes, while in WWTP2 it accounted for only 0.6%. Members of the genera Zoogloea and Thiothrix , aerobic bacteria capable of denitrification, often occur in ASs 57 , 66 , 67 . Both genera were more abundant in WWTPs employing aerobic process.…”